13-112182341-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_944288.1(LOC105370370):n.1403G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.258 in 152,010 control chromosomes in the GnomAD database, including 5,726 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.26 (5726 hom., cov: 33)
• Consequence: LOC105370370 XR_944288.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.818

Genes affected

LOC105370370 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.472 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370370	XR_944288.1	n.1403G>A		non_coding_transcript_exon_variant	4/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.258 AC: 39173 AN: 151892 Hom.: 5715 Cov.: 33

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.188

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.225

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.258 AC: 39218 AN: 152010 Hom.: 5726 Cov.: 33 AF XY: 0.261 AC XY: 19401 AN XY: 74306

Gnomad4 AFR AF: 0.369

Gnomad4 AMR AF: 0.237

Gnomad4 ASJ AF: 0.161

Gnomad4 EAS AF: 0.488

Gnomad4 SAS AF: 0.284

Gnomad4 FIN AF: 0.185

Gnomad4 NFE AF: 0.194

Gnomad4 OTH AF: 0.233

Alfa AF: 0.202 Hom.: 6636

Bravo AF: 0.263

Asia WGS AF: 0.392 AC: 1361 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	1.1
Dann	Benign	0.42

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs9324268; hg19: chr13-112836655;